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- PDB-4u2w: Atomic resolution crystal structure of HV-BBI protease inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 4u2w
TitleAtomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin
Components
  • Bowman-Birk trypsin inhibitor
  • Cationic trypsin
KeywordsHydrolase/inhibitor / inhibitor / Hydrolase-inhibitor complex
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / defense response / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Frog antimicrobial peptide, ranacyclin-type, Ranidae / Frog antimicrobial peptide / Frog antimicrobial peptide, propeptide / Frog skin active peptide family signal and propeptide / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. ...Frog antimicrobial peptide, ranacyclin-type, Ranidae / Frog antimicrobial peptide / Frog antimicrobial peptide, propeptide / Frog skin active peptide family signal and propeptide / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Bowman-Birk trypsin inhibitor / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
Odorrana versabilis (bamboo leaf odorous frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsGrudnik, P. / Golik, P. / Malicki, S. / Debowski, D. / Legowska, A. / Rolka, K. / Dubin, G.
Funding support Poland, 2items
OrganizationGrant numberCountry
NCNUMO-2011/01/D/NZ1/01169 Poland
NCNUMO-2011/01/B/ST5/03772 Poland
CitationJournal: Proteins / Year: 2015
Title: Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin.
Authors: Grudnik, P. / Debowski, D. / Legowska, A. / Malicki, S. / Golik, P. / Karna, N. / Rolka, K. / Dubin, G.
History
DepositionJul 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Bowman-Birk trypsin inhibitor
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,85413
Polymers25,1602
Non-polymers69511
Water6,287349
1
B: Bowman-Birk trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)1,8351
Polymers1,8351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,01912
Polymers23,3241
Non-polymers69511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.738, 62.993, 68.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide / Protein , 2 types, 2 molecules BA

#1: Protein/peptide Bowman-Birk trypsin inhibitor


Mass: 1835.262 Da / Num. of mol.: 1 / Fragment: UNP residues 46-61 / Source method: obtained synthetically
Source: (synth.) Odorrana versabilis (bamboo leaf odorous frog)
References: UniProt: B1VC43
#2: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 4 types, 360 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: sodium acetate trihydrate (0,1 M) at pH 4.6, amonium sulfate (0.3 M) and polyethylene glycol 8000 (30%)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→46.51 Å / Num. obs: 142495 / % possible obs: 98.09 % / Redundancy: 13 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.57
Reflection shellResolution: 1→1.036 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 6.05 / % possible all: 94.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SFI

1sfi


Resolution: 1→46.51 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.289 / SU ML: 0.007 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.10434 7151 5 %RANDOM
Rwork0.09527 ---
obs0.09573 135158 97.96 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 10.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å20 Å2
2--0.04 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 1→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 41 349 2122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191929
X-RAY DIFFRACTIONr_bond_other_d0.0020.021782
X-RAY DIFFRACTIONr_angle_refined_deg2.0151.9572622
X-RAY DIFFRACTIONr_angle_other_deg2.1893.0014119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1275262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51925.71463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.7215292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.788152
X-RAY DIFFRACTIONr_chiral_restr0.2020.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212249
X-RAY DIFFRACTIONr_gen_planes_other0.010.02419
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0510.791017
X-RAY DIFFRACTIONr_mcbond_other1.0350.7891015
X-RAY DIFFRACTIONr_mcangle_it1.3181.1961289
X-RAY DIFFRACTIONr_mcangle_other1.321.1961290
X-RAY DIFFRACTIONr_scbond_it2.2570.964912
X-RAY DIFFRACTIONr_scbond_other2.2570.964912
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5011.3751334
X-RAY DIFFRACTIONr_long_range_B_refined7.7299.2372548
X-RAY DIFFRACTIONr_long_range_B_other5.6877.7742342
X-RAY DIFFRACTIONr_rigid_bond_restr10.97733711
X-RAY DIFFRACTIONr_sphericity_free48.401592
X-RAY DIFFRACTIONr_sphericity_bonded14.39353932
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.144 524 -
Rwork0.127 9499 -
obs--94.29 %

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